Multiple holes really shouldn't be a problem in a standard combustion as long as you are talking about screw size holes and not 2"ers.
Holes in the chamber, where there isn't two layers of PVC, should be fine, again, as long as you are talking about screw size holes and not a 2"ers.
It is pretty easy to patch holes in pvc... For example, to patch a hole in a 3"ID chamber, cut a 2 or 3" long piece of 3" pipe in half (so it looks like a C in cross section). Boil the piece in water for a couple minutes then pull it out and press against a piece of scrap 3" pipe and plunge the whole thing into cool water. PVC has a very low heat capacity, so even when boiling water hot you can usually handle it with bare hands, though you'll need something to reach into the boiling water to grab it with. Once the PVC has cooled, remove it from the scrap pipe. It'll probably spring closed a bit but that's OK. (This technique will enlarge the patch pipe so the new ID is about the same as pipe OD, it can also enlarge the patch ID to the OD of a fitting.)
Get a big-ass hose clamp and your PVC primer and glue. Clean and prime the "C" and the pipe. Put the "C" in place and quickly get the hose clamp on it to hold it. You want the hose clamp fairly tight but not so tight that all of the glue is squeezed out from between the two parts. Let the glue dry for at least 12hrs, 24hrs would be better. Remove the hose clamp and, ta da, you've patched your chamber. The patch should be more than strong enough for a standard combustion.
This same technique could be used to reinforce the chamber for spark electrodes if you are paranoid about weakening the chamber. This technique is also handy for increaseing the wall thickness so that threaded components have more plastic to bite into to create a better pressure seal.